Software and Resources

Please see the research data page for our journal article supplements.

Many of our projects have an accompanying GitHub repository.


Gemma: https://gemma.msl.ubc.ca

Gemma is a system for analyzing genomics data using meta-analysis techniques.


ErmineJ: https://erminej.msl.ubc.ca

ErmineJ performs analyses of gene sets in expression microarray data. A typical goal is to determine whether particular biological pathways are “doing something interesting” in the data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ.


NeuroExpresso: http://neuroexpresso.org

NeuroExpresso is a web-based application designed to facilitate the visualization of gene expression in mouse brain cell types.


NeuroElectro: https://neuroelectro.org

NeuroElectro is a web-based database that stores measurements of basic biophysical properties from diverse neuron types throughout the nervous system.


VariCarta: https://varicarta.msl.ubc.ca

VariCarta is a database of human DNA genetic variants found in individuals diagnosed with Autism Spectrum Disorder (ASD) and reported in peer-reviewed scientific literature.


RDMM Registry: https://register.rare-diseases-catalyst-network.ca

The RDMM Registry collects information on model organism researchers and the specific genes they study. The registry is the mechanism by which the RDMM Network will find potential matches of model organism researchers to human rare disease researchers.


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GOtrack: https://gotrack.msl.ubc.ca

GOtrack is a user-friendly tool to browse the development of gene product annotations. GOtrack currently supports annotation data for 14 different organisms.


Phenocarta: https://gemma.msl.ubc.ca/phenotypes.html

Phenocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations.
Formerly known as Neurocarta.


Expression platform annotations: https://gemma.msl.ubc.ca/annots

We offer a comprehensive set of microarray platform annotation files (as well as files compatible with RNA-seq analysis), generated using Gemma. The files available for download can be used with ermineJ.


Matrix2png: https://matrix2png.msl.ubc.ca

Matrix2png is a simple but powerful program for making visualizations of microarray data and many other data types. It generates PNG formatted images from text files of data. It is fast,easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. Our group has found it useful for imaging all kinds of matrix-based data, not just microarray data. A web interface is included.


Gist: https://svm.msl.ubc.ca

Gist contains software tools for support vector machine classification and for kernel principal components analysis. Gist was developed with Bill Noble.